The midfielders have been battling to be fit for the last-16 second leg in the French capital and both missed Saturday's 3-1 LaLiga win over Getafe.
Kroos, who particularly impressed in Madrid's 3-1 first-leg win, has been struggling due to a knee ligament sprain, while Modric has a hamstring problem.
However, both returned to training on Sunday and will travel to France for the showdown with Unai Emery's men.
Speaking on Saturday, Zidane said he was unsure if they would be fully fit but was not worried about the prospect of their absence.
"I will never regret injuries," he said. "If they can't be with us, other players will play. The only thing we have is to look at Tuesday and see who we are going to go with.
"We have two days to see how Luka and Toni are. I'm not going to tell you what I'm going to do and what we have planned.
"What I want is for all of us to travel. I hope everyone trains on Monday, but I don't know."